Bank of America admitted to skimming off the top from retirees — again.

The country’s No. 2 lender has now paid a total of about $90 million in fines and restitution for ripping off charities and small business retirement plans through 2011, according to the Financial Industry Regulatory Authority, the self-funded regulator for US brokers.

The latest fine from the watchdog group — about $32.4 million on Monday — included $24.4 million in restitution to customers, including small business’ retirement accounts.

Merrill Lynch, which was acquired by BofA in 2009, added extra mutual-fund charges for small business retirement plans for five years, even after discovering that it shouldn’t, the watchdog said.

“From at least January 2006 through December 2011, Merrill Lynch disadvantaged tens of thousands of small business retirements plan customers,” according to the settlement.

The fees were applied to some of the most popular companies managing mutual funds, from Fidelity to Pimco, the settlement said.

“It’s nothing on their end — it’s on us,” said Bill Halldin, a BofA spokesman.

Bank of America didn’t admit or deny guilt in the charges.

The charges, which the bank calls “discrepancies,” weren’t in individual brokerage accounts or in IRAs, Halldin said.

The skimming affected 6,800 accounts for charities and 41,000 for small businesses, Finra said.

“[I]nvestors must be able to trust that their brokerage firm will offer the lowest-cost share classes available to them,” Brad Bennett, Finra’s head of enforcement, said in a release.

On top of the restitution came $8 million in fines.

Earlier, the Charlotte, NC, bank paid about $65 million to make charities financially whole.

The fine comes as the bank is reportedly facing $17 billion in fines for its role in selling bad mortgage-backed securities.

Those proposed fines, which the bank is negotiating with US prosecutors, would likely be the largest fine ever for a US bank, after JPMorgan Chase paid $13 billion last year to settle similar charges without admitting or denying guilt.

BofA had spotted the fees but relied on the Merrill Lynch financial adviser handling each client account to determine if it should get sales charges waived on mutual-fund purchases, Finra said.

But the bank “failed to adequately supervise the sale of these products, or properly train or notify the advisers about lower-cost alternatives.”

Shares of the bank were down more than 1 percent, to $15.28, at the end of trading on Monday.